Research Program

Studies in my laboratory focus on molecular biology and immunopathogenesis of two different viral pathogens, the vesicular stomatitis virus (VSV), a non-segmented negative-strand RNA virus in the family Rhabdoviridae and order Mononagavirales, and the porcine reproductive and respiratory syndrome virus (PRRSV), a positive-strand RNA virus in the family Arteriviridae and order Nidovirales. VSV has served as an excellent paradigm for many negative-strand RNA viruses (some of which are important human pathogens, such as respiratory syncytial, rabies, measles, and parainfluenza, hemorrhagic bunya and arenaviruses) to understand the basic mechanisms of the genetic expression of this group of viruses. PRRSV is an economically important pathogen, causing serious diseases in swine worldwide. Understanding the mechanism(s) of gene expression and its regulation as well as pathogenesis is essential for identifying virus-specific targets for therapeutic intervention in controlling infection by these viruses.

Using VSV, we had previously developed a completely cDNA-based reverse genetic system (Cell, 69:1011-1020, 1992), which has allowed us to introduce specific genetic alterations into the genome of VSV and its defective interfering particles and examine the effects of these alterations on transcription and replication of the viral genomes. The system laid the foundation for genetic manipulation of all negative-strand RNA viruses and has been used extensively by investigators worldwide to generate infectious molecular clones of the negative-strand RNA viruses. Using the system, previous studies from our laboratory addressed three major areas of research: (1) understand the role of nucleotide sequences within the viral genome that control transcription and replication processes; (2) understand structure-function relationships of the viral proteins involved in genome replication, transcription, and virus assembly; and (3) generate and characterize recombinant VSV encoding heterologous viral proteins for vaccine development.

In recent studies, we have described recombinant VSV with a fluorescently tagged P protein (PeGFP fusion protein) to examine intracellular transport of viral nucleocapsids from the sites of synthesis to sites of virus assembly (JVI, 80:6368-6377, 2006). Furthermore, we have generated dual-fluorescent viruses, which have been used to examine by live cell imaging, the entry and uncoating as well as assembly of the viral nucleocapsids in infected cells (JVI, 83:2611-2622, 2009). To understand the regulation of viral genome transcription and replication, we employed structure-guided mutational studies on the viral nucleocapsid protein and have shown (JVI, 83:5525-5534, 2009) that the nucleocapsid protein structure and the resulting nucleocapsid (N-RNA) template are key determinants of N-RNA template functions (transcription and replication). Further studies are being carried out to understand how the nucleocapsid protein and the viral polymerase interactions modulate the transcription and replication functions of the viral template.

To understand the role of cellular functions in regulating viral replication, in collaboration with Dr. Han’s group at Scripps Research Institute at La Jolla, San Diego, we have recently demonstrated that mammalian dicer plays an integral role in innate antiviral immunity to VSV (Immunity, 27:123-134, 2007) through generation of specific microRNAs. We are currently examining the role of host cell functions in viral genome replication by employing genome-wide siRNA screens. A human genome-wide siRNA screening study completed recently for VSV (Proc. Natl. Acad. Sci., USA, In Press, 2011) has identified many important cellular pathways and host cell factors required for infection and replication of VSV. Most interestingly, these studies have identified coatomer protein complex I (COPI) being critically involved in gene expression of VSV as well as two other cytoplasmically replicating negative-strand RNA viruses, the lymphocytic choriomeningitis virus (LCMV) and the human parainfluenza virus type 3 (HPIV3). Further studies have also identified cellular poly(C) binding proteins as important regulators of VSV gene expression (JVI, 85: 9459-9471, 2011). Current studies are directed at understanding of the mechanisms of the involvement of these cellular proteins and pathways in VSV gene expression.

For studies related to PRRSV replication and immune response in infected pigs and cultured cells, we first the nucleotide sequence of the approximately 15.5 kilobase RNA genome and assembled a cDNA clone of the entire viral genome from which infectious virus could be readily recovered (Virology, 325:308-319, 2004). Using this infectious cDNA clone, we are addressing several questions regarding replication and pathogenesis of this important swine pathogen. We have shown that the PRRSV evades host cells’ immune response by employing “glycan shielding” mechanism (JVI, 80:3994-4004, 2006; JVI, 85:5555-5564, 2011), which will have significant impact on PRRSV vaccine development. We have also constructed an infectious clone of a vaccine strain of PRRSV (Vaccine, 24:7071-80, 2006) and by generating chimeric viruses between the highly pathogenic strain and the attenuated vaccine strain we have mapped the regions of the viral genome critical for virulence and attenuation of PRRSV (Virology, 380:371-378, 2008). Our studies have identified the viral glycoproteins that interact with the receptor for entry of the virus into the host cells (JVI, 84:1731-1740, 2010; Virology, 410:385-394, 2011). Studies are being conducted to block these interactions to reduce virus infections. We have recently shown that several of the PRRSV nonstructural proteins possess the inherent ability to suppress the host cell’s innate immune response (JVI, 84:1574-1584, 2010; Virology, 406: 270-279, 2010; JVI, 85(24), In Press, 2011). These studies along with other ongoing studies in our laboratory in collaboration with the laboratory of Dr. F. A. Osorio position us to generate second generation differential PRRSV vaccines by reverse genetic methods.